Converting cryosparc to relion

1 – run cryosparc2star in the directory of interest, with the .cs particle file. Make sure to use the —relion2 flag. 

csparc2star.py DrmABDNAcryosparc_P251_J73_008_particles.cs cryosparc-particles.star –relion2

2 – change .mrc to .mrcs within star file 

sed -i ‘s/.mrc/.mrcs/g’ p205_j279_particles.star

3 – Create new extract job directory corresponding to the one in the cryosparc-particles.star file (use vi cryosparc-particles.star to inspect)

4 – Make symbolic link in new directory 

ln -s /EM/cryosparc/JackBravo/P205/J210/extract/*.mrc .

5 – rename symbolically linked mrc files to mrcs. Do this on javelina or kraken. 

rename s/mrc/mrcs/ *.mrc

6 – run relion! Start a refine job using your cryosparc map as a reference.